The pre-mixed mortar has no acrylic. You'll need to add your own.
Most people do not use it at all.
I'll use bags of pre-mixed I guess. Do I understand correctly that I can use that same mix to grout as I go if I decide to do that? I probably won't though because I'm not crazy about gray and would really like to add an earth tone colorant to the grout. If I can use pre-mix for grouting, is adding colorant as simple as it would seem to be?
When you 'wash' your grout that is when you use a wet sponge and clean the wet mortar off the adjoining surfaces of the stone.
I see - but I'm still unclear about "sealing, resealing".
There will be no buttering of the stones ( jedi hand wave ).
That's a relief - was picturing morter dropping off buttered stones while in transit to their landing spot, making a mess of "cosmic" proportons 
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Mark around the stones while they are sitting on the slab before you apply any mortar. Like one of those crime scene body chalk outlines!
Apply your mortar inside you lines.
That makes so much sense - the slab is broom surfaced so I guess a fat lead carpenter's pencil or chalk will work, eh?
Do you have your flagstone? Unless one side of it is 'guaged' or flat from the quarry it will be varying in thickness. If not, it is OK to set either side up. ( there is no top or bottom )
I looked at what I want at the stone yard but haven't ordered it yet. It's not been guaged but can be laid either surface up:
Category: Flagstone / Random
Description: Light silver base with splashes of gold flecked with mica.
I'll probably buy 2 1/2 tons which will hopefully allow for breakage and leave some that I'll use in a future water feature that I'm planning.
Variations of 3/4" to 2" are not uncommon...On the same piece at times!
It's time consuming HARD work. DO NOT RUSH!!
Finally - hearing it from a pro - I'll BET it's hard work and I won't be rushing.
The Makita hand held diamond saw has no place on this job. Save it!
An angle grinder or Skil saw with a dry diamond blade is the way to go.
Great. I own a Skil saw. Would buying an angle grinder be a lot better?
You'll need a 'rock hammer'. It has two ends.
Which end should I use?
One end has a square, heavy head for breaking and the other has a long flat blade for chipping or splitting pieces.
Also, let you slab cure out for a couple more weeks before doing anything.
Yeh, it'll be a while. I've got a 10'x20' garden studio about to be built first on another slab 14' off my patio slab
KT